ORCID Profile
0000-0001-6052-6854
Current Organisation
Argonne National Laboratory
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Publisher: Wiley
Date: 12-07-2012
DOI: 10.1002/ECE3.298
Publisher: Elsevier BV
Date: 11-2020
Publisher: Springer Science and Business Media LLC
Date: 29-01-2016
DOI: 10.1038/NCOMMS10511
Abstract: Late Quaternary megafauna extinctions impoverished mammalian ersity worldwide. The causes of these extinctions in Australia are most controversial but essential to resolve, because this continent-wide event presaged similar losses that occurred thousands of years later on other continents. Here we apply a rigorous metadata analysis and new ensemble-hindcasting approach to 659 Australian megafauna fossil ages. When coupled with analysis of several high-resolution climate records, we show that megafaunal extinctions were broadly synchronous among genera and independent of climate aridity and variability in Australia over the last 120,000 years. Our results reject climate change as the primary driver of megafauna extinctions in the world’s most controversial context, and instead estimate that the megafauna disappeared Australia-wide ∼13,500 years after human arrival, with shorter periods of coexistence in some regions. This is the first comprehensive approach to incorporate uncertainty in fossil ages, extinction timing and climatology, to quantify mechanisms of prehistorical extinctions.
Publisher: Wiley
Date: 08-08-2021
Abstract: Principal component analysis (PCA) is a powerful tool for the analysis of population structure, a genetic property that is essential to understand the evolutionary processes driving biological ersification and (pre)historical colonizations, migrations and extinctions. In the current era of high‐throughput sequencing technologies, population structure can be quantified from scores of genetic markers across hundreds to thousands of genomes. However, these big genomic datasets pose substantial computing and analytical challenges. We present the r package smartsnp for fast and user‐friendly computation of PCA on single‐nucleotide polymorphism (SNP) data. Inspired by the current field‐standard software EIGENSOFT, smartsnp includes appropriate SNP scaling for genetic drift and allows projection of ancient s les onto a modern genetic space while also providing permutation‐based multivariate tests for population differences in genetic ersity (both location and dispersion). Our extensive benchmarks show that smartsnp 's PCA is 2–4 times faster than EIGENSOFT's SMARTPCA algorithm across a wide range of s le and SNP sizes. All four smartsnp functions ( smart_pca , smart_permanova , smart_permdisp and smart_mva ) process datasets with up to 100 s les and 1 million simulated SNPs in less than 30 s and accurately recreate previously published SMARTPCA of ancient‐human and wolf genotypes. The package smartsnp provides fast and robust multivariate ordination and hypothesis testing for big genomic data that is also suitable for ancient and low‐coverage modern DNA. The simple implementation should appeal to biological conservation, evolutionary, ecological and (palaeo)genomic researchers, and be useful for phenotype, ancestry and lineage studies.
Publisher: No publisher found
Date: 2021
DOI: 10.1098/RSOS.201351
Publisher: Edward Elgar Publishing
Date: 31-10-2014
Publisher: Wiley
Date: 24-10-2013
Abstract: Metabolic theory predicts that demographic rates can be expressed as a function of environmental temperature. Amarasekare & Coutinho (2013) build a novel matrix model where demographic rates (fertility, mortality, development) vary according to expected rates of climate warming. They challenge recent studies that claim low population viability of tropical species based on rmax estimated from the Euler-Lotka equation, because the latter assumes a constant stage distribution that is unrealistic under fast rates of warming and for organisms with long development. In those cases, the measurement of the temperature responses of life-history traits could be based in niche theory.
Publisher: The Royal Society
Date: 07-07-2014
Abstract: Geographical range dynamics are driven by the joint effects of abiotic factors, human ecosystem modifications, biotic interactions and the intrinsic organismal responses to these. However, the relative contribution of each component remains largely unknown. Here, we compare the contribution of life-history attributes, broad-scale gradients in climate and geographical context of species’ historical ranges, as predictors of recent changes in area of occupancy for 116 terrestrial British breeding birds (74 contractors, 42 expanders) between the early 1970s and late 1990s. Regional threat classifications demonstrated that the species of highest conservation concern showed both the largest contractions and the smallest expansions. Species responded differently to climate depending on geographical distribution—northern species changed their area of occupancy (expansion or contraction) more in warmer and drier regions, whereas southern species changed more in colder and wetter environments. Species with slow life history (larger body size) tended to have a lower probability of changing their area of occupancy than species with faster life history, whereas species with greater natal dispersal capacity resisted contraction and, counterintuitively, expansion. Higher geographical fragmentation of species' range also increased expansion probability, possibly indicating a release from a previously limiting condition, for ex le through agricultural abandonment since the 1970s. After accounting statistically for the complexity and nonlinearity of the data, our results demonstrate two key aspects of changing area of occupancy for British birds: (i) climate is the dominant driver of change, but direction of effect depends on geographical context, and (ii) all of our predictors generally had a similar effect regardless of the direction of the change (contraction versus expansion). Although we caution applying results from Britain's highly modified and well-studied bird community to other biogeographic regions, our results do indicate that a species' propensity to change area of occupancy over decadal scales can be explained partially by a combination of simple allometric predictors of life-history pace, average climate conditions and geographical context.
Publisher: Oxford University Press (OUP)
Date: 18-02-2014
Publisher: Oxford University Press (OUP)
Date: 03-2019
Publisher: Wiley
Date: 17-10-2008
Publisher: Oxford University Press (OUP)
Date: 14-04-2014
Publisher: Springer Science and Business Media LLC
Date: 31-05-2012
DOI: 10.1007/S00442-012-2347-3
Abstract: The concept of density dependence represents the effect of changing population size on demographic rates and captures the demographic role of social and trophic mechanisms (e.g. competition, cooperation, parasitism or predation). Ecologists have coined more than 60 terms to denote different statistical and semantic properties of this concept, resulting in a formidable lexicon of synonymies and polysemies. We have examined the vocabulary of density dependence used in the modern ecological literature from the foundational lexicon developed by Smith, Allee, Haldane, Neave and Varley. A few simple rules suffice to abate terminological inconsistency and to enhance the biological meaning of this important concept. Correct citation of original references by ecologists and research journals could ameliorate terminological standards in our discipline and avoid linguistic confusion of mathematically and theoretically complex patterns.
Publisher: Springer Science and Business Media LLC
Date: 19-07-2016
Abstract: The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of in idual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.
Publisher: Informa UK Limited
Date: 22-02-2010
Publisher: Public Library of Science (PLoS)
Date: 03-03-2011
Publisher: Elsevier BV
Date: 10-1998
Publisher: Cold Spring Harbor Laboratory
Date: 22-09-2021
DOI: 10.1101/2021.09.19.460939
Abstract: Analysis of long-term trends in abundance provide insights into population dynamics. Population growth rates are the emergent interplay of fertility, survival, and dispersal, but the density feedbacks on some vital rates (component) can be decoupled from density feedback on population growth rates (ensemble). However, the mechanisms responsible for this decoupling are poorly understood. We simulated component density feedbacks on survival in age-structured populations of long-living vertebrates and quantified how imposed nonstationarity (density-independent mortality and variation in carrying-capacity) modified the ensemble feedback signal estimated from logistic-growth models to the simulated abundance time series. The statistical detection of ensemble density feedback was largely unaffected by density-independent processes, but catastrophic and proportional mortality eroded the effect of density-dependent survival on ensemble-feedback strength more strongly than variation in carrying capacity. Thus, phenomenological models offer a robust approach to capture density feedbacks from nonstationary census data when density-independent mortality is low.
Publisher: Magnolia Press
Date: 23-12-2003
Abstract: A new species of hypogean cirolanid isopod, Typhlocirolana troglobia sp. nov. is described, from specimens obtained during speleological explorations of a karstic cave in the Miravet Ravine, Spain. Typhlocirolana troglobia sp. nov. can be distinguished from all other species in the genus by the combination of the following characters: lack of sexual dimorphism of pereopod 7, absence of sexual dimorphism in the chaetotaxy of the propodus of pereopod 3, and the excavate and serrate appendix masculina apex.
Publisher: Wiley
Date: 08-01-2020
Publisher: The Royal Society
Date: 10-02-2016
Abstract: During the Pleistocene, Australia and New Guinea supported a rich assemblage of large vertebrates. Why these animals disappeared has been debated for more than a century and remains controversial. Previous synthetic reviews of this problem have typically focused heavily on particular types of evidence, such as the dating of extinction and human arrival, and have frequently ignored uncertainties and biases that can lead to misinterpretation of this evidence. Here, we review erse evidence bearing on this issue and conclude that, although many knowledge gaps remain, multiple independent lines of evidence point to direct human impact as the most likely cause of extinction.
Publisher: Wiley
Date: 13-05-2020
Publisher: American Physical Society (APS)
Date: 24-08-2020
Publisher: Public Library of Science (PLoS)
Date: 11-03-2014
Publisher: Wiley
Date: 04-2023
DOI: 10.1002/ECE3.10010
Abstract: Analysis of long‐term trends in abundance of animal populations provides insights into population dynamics. Population growth rates are the emergent interplay of inter alia fertility, survival, and dispersal. However, the density feedbacks operating on some vital rates (“component feedback”) can be decoupled from density feedbacks on population growth rates estimated using abundance time series (“ensemble feedback”). Many of the mechanisms responsible for this decoupling are poorly understood, thereby questioning the validity of using logistic‐growth models versus vital rates to infer long‐term population trends. To examine which conditions lead to decoupling, we simulated age‐structured populations of long‐lived vertebrates experiencing component density feedbacks on survival. We then quantified how imposed stochasticity in survival rates, density‐independent mortality (catastrophes, harvest‐like removal of in iduals) and variation in carrying capacity modified the ensemble feedback in abundance time series simulated from age‐structured populations. The statistical detection of ensemble density feedback from census data was largely unaffected by density‐independent processes. Long‐term population decline caused from density‐independent mortality was the main mechanism decoupling the strength of component versus ensemble density feedbacks. Our study supports the use of simple logistic‐growth models to capture long‐term population trends, mediated by changes in population abundance, when survival rates are stochastic, carrying capacity fluctuates, and populations experience moderate catastrophic mortality over time.
Publisher: Elsevier BV
Date: 03-2023
Publisher: Elsevier BV
Date: 10-2015
Publisher: Wiley
Date: 02-11-2018
Abstract: Research addressing the effects of global warming on the distribution and persistence of species generally assumes that population variation in thermal tolerance is spatially constant or overridden by interspecific variation. Typically, this rationale is implicit in sourcing one critical thermal maximum (CT
Publisher: The Biological Society of Washington
Date: 04-2005
Publisher: Wiley
Date: 07-2012
DOI: 10.1890/11-1415.1
Abstract: A component density feedback represents the effect of change in population size on single demographic rates, whereas an ensemble density feedback captures that effect on the overall growth rate of a population. Given that a population's growth rate is a synthesis of the interplay of all demographic rates operating in a population, we test the hypothesis that the strength of ensemble density feedback must augment with increasing strength of component density feedback, using long‐term censuses of population size, fertility, and survival rates of 109 bird and mammal populations (97 species). We found that compensatory and depensatory component feedbacks were common (each detected in ∼50% of the demographic rates). However, component feedback strength only explained % of the variation in ensemble feedback strength. To explain why, we illustrate the different sources of decoupling between component and ensemble feedbacks. We argue that the management of anthropogenic impacts on populations using component feedbacks alone is ill‐advised, just as managing on the basis of ensemble feedbacks without a mechanistic understanding of the contributions made by its components and environmental variability can lead to suboptimal decisions.
Publisher: Springer Science and Business Media LLC
Date: 07-03-2007
Publisher: Springer Science and Business Media LLC
Date: 13-08-2020
DOI: 10.1038/S41597-020-00598-9
Abstract: Genetic data are a crucial and exponentially growing resource across all biological sciences, yet curated databases are scarce. The widespread occurrence of sequence and (meta)data errors in public repositories calls for comprehensive improvements of curation protocols leading to robust research and downstream analyses. We collated and curated all available GenBank cytochrome-b sequences for hibians, a benchmark marker in this globally declining vertebrate clade. The Amphibia’s Curated Database of Cytochrome-b (ACDC) consists of 36,514 sequences representing 2,309 species from 398 genera (median = 2 with 50% interquartile ranges of 1–7 species/genus). We updated the taxonomic identity of ,800 sequences (ca. 13%) and found 2,359 (6%) conflicting sequences with 84% of the errors originating from taxonomic misidentifications. The database (accessible at 0.6084/m9.figshare.9944759 ) also includes an R script to replicate our study for other loci and taxonomic groups. We provide recommendations to improve genetic-data quality in public repositories and flag species for which there is a need for taxonomic refinement in the face of increased rate of hibian extinctions in the Anthropocene.
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 2001
End Date: 2003
Funder: British Ecological Society
View Funded ActivityStart Date: 2007
End Date: 2008
Funder: British Ecological Society
View Funded ActivityStart Date: 2008
End Date: 2012
Funder: Australian Research Council
View Funded ActivityStart Date: 2013
End Date: 2015
Funder: Fifth Framework Programme
View Funded ActivityStart Date: 2014
End Date: 2015
Funder: British Ecological Society
View Funded Activity